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Hi There,
I've used MeGAMerge to merge two assemblies of the same data (https://github.com/LANL-Bioinformatics/MeGAMerge), but merging has produced many ambiguous bases. I have good read coverage, so I'd like to use read mapping to call the ambiguous bases (likely SNPs) based on majority rules. Can someone recommend a strategy for this? I've written a script to identify the location of all ambiguous bases and use 'samtools view' to grab all the reads that map to that location, and I could write a script to parse those reads at that specific position, but I hesitate because I'm sure someone has already solved this problem.
p.s. I've use pilon's fix '--amb' function, which should have done the trick, but the output is identical to my input. (https://github.com/broadinstitute/pilon/wiki)
Thanks in advance,
Roli
I've used MeGAMerge to merge two assemblies of the same data (https://github.com/LANL-Bioinformatics/MeGAMerge), but merging has produced many ambiguous bases. I have good read coverage, so I'd like to use read mapping to call the ambiguous bases (likely SNPs) based on majority rules. Can someone recommend a strategy for this? I've written a script to identify the location of all ambiguous bases and use 'samtools view' to grab all the reads that map to that location, and I could write a script to parse those reads at that specific position, but I hesitate because I'm sure someone has already solved this problem.
p.s. I've use pilon's fix '--amb' function, which should have done the trick, but the output is identical to my input. (https://github.com/broadinstitute/pilon/wiki)
Thanks in advance,
Roli